[gmx-users] Umbrella_pull_simulation

[shahid nayeem]

I am attaching a profile.xvg and histo.xvg. In each window 10ns sampling
was done. The umbrella pullcode used is as follows.
; Pull code
pull            = umbrella
pull_geometry   = distance  ; simple distance increase
pull_dim        = Y    N Y
pull_vec1       = 0.75 0 1
pull_start      = yes       ; define initial COM distance > 0
pull_ngroups    = 1
pull_group0     = Chain_B
pull_group1     = Chain_A
pull_rate1      = 0.01      ; 0.01 nm per ps = 10 nm per ns
pull_k1         = 1000      ; kJ mol^-1 nm^-2

Please tell me my profile.xvg and histo.xvg are fine or not. In profile.xvg
why i am not getting smooth convergence.
Shahid Nayeem

On Mon, Feb 20, 2012 at 10:48 PM, shahid nayeem <msnayeem at gmail.com> wrote:

> I am attaching a profile.xvg and histo.xvg. In each window 10ns sampling
> was done. The umbrella pullcode used is as follows.
> ; Pull code
> pull            = umbrella
> pull_geometry   = distance  ; simple distance increase
> pull_dim        = Y    N Y
> pull_vec1       = 0.75 0 1
> pull_start      = yes       ; define initial COM distance > 0
> pull_ngroups    = 1
> pull_group0     = Chain_B
> pull_group1     = Chain_A
> pull_rate1      = 0.01      ; 0.01 nm per ps = 10 nm per ns
> pull_k1         = 1000      ; kJ mol^-1 nm^-2
>
> Please tell me my profile.xvg and histo.xvg are fine or not. In
> profile.xvg why i am not getting smooth convergence.
> Shahid Nayeem
>
> On Mon, Feb 20, 2012 at 8:24 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> shahid nayeem wrote:
>>
>>> Thanks Justin
>>> I have pulled one of the chain from an initial COM distance value of
>>> 3.65 A to 7.90 A. When I look this trajectory in VMD I find that the
>>>
>>
>> I will have to assume you mean nm.  Gromacs does not deal in Angstrom,
>> and these distances would be within any sensible short-range cutoff and
>> thus not indicative of actual separation.
>>
>>
>>  chain is completely separated. But even at this separation the
>>> profile.xvg file does not show its convergence to one value. I sent this
>>> file to you earlier.
>>>
>>
>> Sorry, I don't have a photographic memory, nor can I recall if you've
>> ever posted your .mdp file, or at the very least, told us how much sampling
>> you've done in each window.  It may well be that your simulations are
>> simply too short to observe adequate post-equilibration sampling.
>>
>>
>> -Justin
>>
>> --
>> ==============================**==========
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120220/fcd497a8/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: profile.xvg
Type: application/octet-stream
Size: 5549 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120220/fcd497a8/attachment.obj>